arXiv subjects

O. Bénichou

Publications and source records attributed to O. Bénichou.

48 records · Page 3Linked to original sources

arXiv2012

Exact calculations of first-passage quantities on recursive networks

We present general methods to exactly calculate mean-first passage quantities on self-similar networks defined recursively. In particular, we calculate the mean first-passage time and the splitting probabilities associated to a source and one or several targets; averaged quantities over a given set of sources (e.g., same-connectivity nodes) are also derived. The exact estimate of such quantities highlights the dependency of first-passage processes with respect to the source-target distance, which has recently revealed to be a key parameter to characterize transport in complex media. We explicitly perform calculations for different classes of recursive networks (finitely ramified fractals, scale-free (trans)fractals, non-fractals, mixtures between fractals and non-fractals, non-decimable hierarchical graphs) of arbitrary size. Our approach unifies and significantly extends the available results in the field.

cond-mat.stat-mech↗

arXiv2011

Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.

q-bio.BM↗

arXiv2011

Intermittent search strategies

This review examines intermittent target search strategies, which combine phases of slow motion, allowing the searcher to detect the target, and phases of fast motion during which targets cannot be detected. We first show that intermittent search strategies are actually widely observed at various scales. At the macroscopic scale, this is for example the case of animals looking for food ; at the microscopic scale, intermittent transport patterns are involved in reaction pathway of DNA binding proteins as well as in intracellular transport. Second, we introduce generic stochastic models, which show that intermittent strategies are efficient strategies, which enable to minimize the search time. This suggests that the intrinsic efficiency of intermittent search strategies could justify their frequent observation in nature. Last, beyond these modeling aspects, we propose that intermittent strategies could be used also in a broader context to design and accelerate search processes.

cond-mat.stat-mech↗

arXiv2011

Mean first-passage time of surface-mediated diffusion in spherical domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.

cond-mat.stat-mech↗

arXiv2010

Optimal reaction time for surface-mediated diffusion

We present an exact calculation of the mean first-passage time to a small target on the surface of a 2D or 3D spherical domain, for a molecule performing surface-mediated diffusion. This minimal model of interfacial reactions, which explicitly takes into account the combination of surface and bulk diffusion, shows the importance of correlations induced by the coupling of the switching dynamics to the geometry of the confinement, ignored so far. Interestingly, our results show that, in the context of interfacial systems in confinement, the reaction time can be minimized as a function of the desorption rate from the surface, which puts forward a general mechanism of enhancement and regulation of chemical reactivity.

cond-mat.stat-mech↗

arXiv2010

Spontaneous contractility--mediated cortical flow generates cell migration in 3-dimensional environments

We present a generic model of cell motility generated by acto-myosin contraction of the cell cortex. We identify analytically dynamical instabilities of the cortex and show that they trigger spontaneous cortical flows which in turn can induce cell migration in 3-dimensional (3D) environments as well as bleb formation. This contractility--based mechanism, widely independent of actin treadmilling, appears as an alternative to the classical picture of lamellipodial motility on flat substrates. Theoretical predictions are compared to experimental data of tumor cells migrating in 3D matrigel and suggest that this mechanism could be a general mode of cell migration in 3D environments.

q-bio.CB↗

arXiv2010

Optimization of the residence time of a Brownian particle in a spherical subdomain

In this communication, we show that the residence time of a Brownian particle, defined as the cumulative time spent in a given region of space, can be optimized as a function of the diffusion coefficient. We discuss the relevance of this effect to several schematic experimental situations, classified in the nature -- random or deterministic -- both of the observation time and of the starting position of the Brownian particle.

cond-mat.stat-mech↗

arXiv2010

Geometry-controlled kinetics

It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to quantify the kinetics of reactions on all time scales, determining the FPT distribution was deemed so far intractable. Here, we calculate analytically this FPT distribution and show that transport processes as various as regular diffusion, anomalous diffusion, diffusion in disordered media and in fractals fall into the same universality classes. Beyond this theoretical aspect, this result changes the views on standard reaction kinetics. More precisely, we argue that geometry can become a key parameter so far ignored in this context, and introduce the concept of "geometry-controlled kinetics". These findings could help understand the crucial role of spatial organization of genes in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.

cond-mat.stat-mech↗

arXiv2009

Robustness of optimal intermittent search strategies in dimension 1, 2 and 3

Search problems at various scales involve a searcher, be it a molecule before reaction or a foraging animal, which performs an intermittent motion. Here we analyze a generic model based on such type of intermittent motion, in which the searcher alternates phases of slow motion allowing detection, and phases of fast motion without detection. We present full and systematic results for different modeling hypotheses of the detection mechanism in space dimension 1, 2 and 3. Our study completes and extends the results of our recent letter [Loverdo {\it et al.} Nature Physics {\bf 4}, 134 (2008)] and gives the necessary calculation details. In addition, a new modeling of the detection phase is presented. We show that the mean target detection time can be minimized as a function of the mean duration of each phase in dimension 1, 2 and 3. Importantly, this optimal strategy does not depend on the details of the modeling of the slow detection phase, which shows the robustness of our results. We believe that this systematic analysis can be used as a basis to study quantitatively various real search problems involving intermittent behaviors.

cond-mat.stat-mech↗

arXiv2009

Global mean first-passage times of random walks on complex networks

We present a general framework, applicable to a broad class of random walks on complex networks, which provides a rigorous lower bound for the mean first-passage time of a random walker to a target site averaged over its starting position, the so-called global mean first-passage time (GMFPT). This bound is simply expressed in terms of the equilibrium distribution at the target, and implies a minimal scaling of the GMFPT with the network size. We show that this minimal scaling, which can be arbitrarily slow for a proper choice of highly connected target, is realized under the simple condition that the random walk is transient at the target site, and independently of the small-world, scale free or fractal properties of the network. Last, we put forward that the GMFPT to a specific target is not a representative property of the network, since the target averaged GMFPT satisfies much more restrictive bounds, which forbid any sublinear scaling with the network size.

cond-mat.stat-mech↗

arXiv2009

Searching fast for a target on a DNA without falling to traps

Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA. Equilibrium experiments show that indeed regulatory proteins bind tightly to their target site. However, they also find strong binding to other non-specific sites which act as traps that can dramatically increase the time needed to locate the target. This gives rise to a conflict between the speed and stability requirements. Here we suggest a simple mechanism which can resolve this long-standing paradox by allowing the target sites to be located by proteins within short time scales even in the presence of traps. Our theoretical analysis shows that the mechanism is robust in the presence of generic disorder in the DNA sequence and does not require a specially designed target site.

cond-mat.soft↗

arXiv2005

Kinetics of diffusion-limited catalytically-activated reactions: An extension of the Wilemski-Fixman approach

We study kinetics of diffusion-limited catalytically-activated $A + B \to B$ reactions taking place in three dimensional systems, in which an annihilation of diffusive $A$ particles by diffusive traps $B$ may happen only if the encounter of an $A$ with any of the $B$s happens within a special catalytic subvolumen, these subvolumens being immobile and uniformly distributed within the reaction bath. Suitably extending the classical approach of Wilemski and Fixman (G. Wilemski and M. Fixman, J. Chem. Phys. \textbf{58}:4009, 1973) to such three-molecular diffusion-limited reactions, we calculate analytically an effective reaction constant and show that it comprises several terms associated with the residence and joint residence times of Brownian paths in finite domains. The effective reaction constant exhibits a non-trivial dependence on the reaction radii, the mean density of catalytic subvolumens and particles' diffusion coefficients. Finally, we discuss the fluctuation-induced kinetic behavior in such systems.

cond-mat.stat-mech↗